Multi-Level Parallel Network for Brain Tumor Segmentation

Accurate automatic segmentation of gliomas in various sub-regions,including peritumoral edema,necrotic core,and enhancing and non-enhancing tumor core from 3D multimodal MRI images,is challenging because of its highly heterogeneous appearance and shape.Deep convolution neural networks(CNNs)have recently improved glioma segmentation performance.However,extensive down-sampling such as pooling or stridden convolution in CNNs significantly decreases the initial image resolution,resulting in the loss of accurate spatial and object parts information,especially information on the small sub-region tumors,affecting segmentation performance.Hence,this paper proposes a novel multi-level parallel network comprising three different level parallel subnetworks to fully use low-level,mid-level,and high-level information and improve the performance of brain tumor segmentation.We also introduce the Combo loss function to address input class imbalance and false positives and negatives imbalance in deep learning.The proposed method is trained and validated on the BraTS 2020 training and validation dataset.On the validation dataset,ourmethod achieved a mean Dice score of 0.907,0.830,and 0.787 for the whole tumor,tumor core,and enhancing tumor core,respectively.Compared with state-of-the-art methods,the multi-level parallel network has achieved competitive results on the validation dataset.

Salp Swarm Algorithm with Multilevel Thresholding Based Brain Tumor Segmentation Model

Biomedical image processing acts as an essential part of severalmedical applications in supporting computer aided disease diagnosis. MagneticResonance Image (MRI) is a commonly utilized imaging tool used tosave glioma for clinical examination. Biomedical image segmentation plays avital role in healthcare decision making process which also helps to identifythe affected regions in the MRI. Though numerous segmentation models areavailable in the literature, it is still needed to develop effective segmentationmodels for BT. This study develops a salp swarm algorithm with multi-levelthresholding based brain tumor segmentation (SSAMLT-BTS) model. Thepresented SSAMLT-BTS model initially employs bilateral filtering based onnoise removal and skull stripping as a pre-processing phase. In addition,Otsu thresholding approach is applied to segment the biomedical imagesand the optimum threshold values are chosen by the use of SSA. Finally,active contour (AC) technique is used to identify the suspicious regions in themedical image. A comprehensive experimental analysis of the SSAMLT-BTSmodel is performed using benchmark dataset and the outcomes are inspectedin many aspects. The simulation outcomes reported the improved outcomesof the SSAMLT-BTS model over recent approaches with maximum accuracyof 95.95%.

Clinical Knowledge-Based Hybrid Swin Transformer for Brain Tumor Segmentation

Accurate tumor segmentation from brain tissues in Magnetic Resonance Imaging(MRI)imaging is crucial in the pre-surgical planning of brain tumor malignancy.MRI images’heterogeneous intensity and fuzzy boundaries make brain tumor segmentation challenging.Furthermore,recent studies have yet to fully employ MRI sequences’considerable and supplementary information,which offers critical a priori knowledge.This paper proposes a clinical knowledge-based hybrid Swin Transformermultimodal brain tumor segmentation algorithmbased on how experts identify malignancies from MRI images.During the encoder phase,a dual backbone network with a Swin Transformer backbone to capture long dependencies from 3D MR images and a Convolutional Neural Network(CNN)-based backbone to represent local features have been constructed.Instead of directly connecting all the MRI sequences,the proposed method re-organizes them and splits them into two groups based on MRI principles and characteristics:T1 and T1ce,T2 and Flair.These aggregated images are received by the dual-stem Swin Transformer-based encoder branch,and the multimodal sequence-interacted cross-attention module(MScAM)captures the interactive information between two sets of linked modalities in each stage.In the CNN-based encoder branch,a triple down-sampling module(TDsM)has been proposed to balance the performance while downsampling.In the final stage of the encoder,the feature maps acquired from two branches are concatenated as input to the decoder,which is constrained by MScAM outputs.The proposed method has been evaluated on datasets from the MICCAI BraTS2021 Challenge.The results of the experiments demonstrate that the method algorithm can precisely segment brain tumors,especially the portions within tumors.

MRI Brain Tumor Segmentation Using 3D U-Net with Dense Encoder Blocks and Residual Decoder Blocks

The main task of magnetic resonance imaging (MRI) automatic brain tumor segmentation is to automaticallysegment the brain tumor edema, peritumoral edema, endoscopic core, enhancing tumor core and nonenhancingtumor core from 3D MR images. Because the location, size, shape and intensity of brain tumors vary greatly, itis very difficult to segment these brain tumor regions automatically. In this paper, by combining the advantagesof DenseNet and ResNet, we proposed a new 3D U-Net with dense encoder blocks and residual decoder blocks.We used dense blocks in the encoder part and residual blocks in the decoder part. The number of output featuremaps increases with the network layers in contracting path of encoder, which is consistent with the characteristicsof dense blocks. Using dense blocks can decrease the number of network parameters, deepen network layers,strengthen feature propagation, alleviate vanishing-gradient and enlarge receptive fields. The residual blockswere used in the decoder to replace the convolution neural block of original U-Net, which made the networkperformance better. Our proposed approach was trained and validated on the BraTS2019 training and validationdata set. We obtained dice scores of 0.901, 0.815 and 0.766 for whole tumor, tumor core and enhancing tumorcore respectively on the BraTS2019 validation data set. Our method has the better performance than the original3D U-Net. The results of our experiment demonstrate that compared with some state-of-the-art methods, ourapproach is a competitive automatic brain tumor segmentation method.

Brain Tumor Segmentation of HGG and LGG MRI Images Using WFL-Based 3D U-Net

The semantic segmentation of a brain tumor is the essential stage in medical treatment planning. Due to the different characteristics of tumors, one of the main difficulties in image segmentation is the severe imbalance between classes. Also, a dataset with imbalanced classes is a common problem in multimodal 3D brain MRIs. Despite these problems, most studies in brain tumor segmentation are biased toward the overrepresented tumor class (majority class) and ignore the small size tumor class (minority class). In this paper, we propose an improved loss function Weighted Focal Loss (WFL), based on 3D U-Net to enhance the prediction of brain tumor segmentation. Using our proposed loss function (WFL) solves the imbalance between classes and the imbalance between weights by giving higher weights to the minority and lower weights to the majority. After assigning these weights to different pixel values, our work is able to resolve pixel degradation, which is one of the limitations of the loss function during model training. Based on our experiments, the proposed function (WFL) on the 3D U-Net model for high-grade glioma (HGG) and low-grade glioma (LGG) in the Brain Tumor Segmentation Challenge (BraTS) 2019 dataset has shown promising results for tumor core (TC), whole tumor (WT) and enhanced tumor (ET) with average dice scores of HGG: 0.830, 0.913, 0.815 and Dice scores of LGG for TC: 0.731, WT: 0.775 and ET: 0.685. Moreover, we deployed our training on BraTS 2020 in which we obtained mean Dice scores of HGG: TC: 0.843, WT: 0.892, ET: 0.871 and Dice scores of LGG: 0.7501, 0.7985, 0.6103 for TC, WT and ET, respectively.

Multitask Learning with Multiscale Residual Attention for Brain Tumor Segmentation and Classification

Automatic segmentation and classification of brain tumors are of great importance to clinical treatment.However,they are challenging due to the varied and small morphology of the tumors.In this paper,we propose a multitask multiscale residual attention network(MMRAN)to simultaneously solve the problem of accurately segmenting and classifying brain tumors.The proposed MMRAN is based on U-Net,and a parallel branch is added at the end of the encoder as the classification network.First,we propose a novel multiscale residual attention module(MRAM)that can aggregate contextual features and combine channel attention and spatial attention better and add it to the shared parameter layer of MMRAN.Second,we propose a method of dynamic weight training that can improve model performance while minimizing the need for multiple experiments to determine the optimal weights for each task.Finally,prior knowledge of brain tumors is added to the postprocessing of segmented images to further improve the segmentation accuracy.We evaluated MMRAN on a brain tumor data set containing meningioma,glioma,and pituitary tumors.In terms of segmentation performance,our method achieves Dice,Hausdorff distance(HD),mean intersection over union(MIoU),and mean pixel accuracy(MPA)values of 80.03%,6.649 mm,84.38%,and 89.41%,respectively.In terms of classification performance,our method achieves accuracy,recall,precision,and F1-score of 89.87%,90.44%,88.56%,and 89.49%,respectively.Compared with other networks,MMRAN performs better in segmentation and classification,which significantly aids medical professionals in brain tumor management.The code and data set are available at https://github.com/linkenfaqiu/MMRAN.

3D Kronecker Convolutional Feature Pyramid for Brain Tumor Semantic Segmentation in MR Imaging

Brain tumor significantly impacts the quality of life and changes everything for a patient and their loved ones.Diagnosing a brain tumor usually begins with magnetic resonance imaging(MRI).The manual brain tumor diagnosis from the MRO images always requires an expert radiologist.However,this process is time-consuming and costly.Therefore,a computerized technique is required for brain tumor detection in MRI images.Using the MRI,a novel mechanism of the three-dimensional(3D)Kronecker convolution feature pyramid(KCFP)is used to segment brain tumors,resolving the pixel loss and weak processing of multi-scale lesions.A single dilation rate was replaced with the 3D Kronecker convolution,while local feature learning was performed using the 3D Feature Selection(3DFSC).A 3D KCFP was added at the end of 3DFSC to resolve weak processing of multi-scale lesions,yielding efficient segmentation of brain tumors of different sizes.A 3D connected component analysis with a global threshold was used as a post-processing technique.The standard Multimodal Brain Tumor Segmentation 2020 dataset was used for model validation.Our 3D KCFP model performed exceptionally well compared to other benchmark schemes with a dice similarity coefficient of 0.90,0.80,and 0.84 for the whole tumor,enhancing tumor,and tumor core,respectively.Overall,the proposed model was efficient in brain tumor segmentation,which may facilitate medical practitioners for an appropriate diagnosis for future treatment planning.

Kernel sparse representation for MRI image analysis in automatic brain tumor segmentation

The segmentation of brain tumor plays an important role in diagnosis, treatment planning, and surgical simulation. The precise segmentation of brain tumor can help clinicians obtain its location, size, and shape information. We propose a fully automatic brain tumor segmentation method based on kernel sparse coding. It is validated with 3D multiple-modality magnetic resonance imaging(MRI). In this method, MRI images are pre-processed first to reduce the noise, and then kernel dictionary learning is used to extract the nonlinear features to construct five adaptive dictionaries for healthy tissues, necrosis, edema, non-enhancing tumor, and enhancing tumor tissues. Sparse coding is performed on the feature vectors extracted from the original MRI images, which are a patch of m×m×m around the voxel. A kernel-clustering algorithm based on dictionary learning is developed to code the voxels. In the end, morphological filtering is used to fill in the area among multiple connected components to improve the segmentation quality. To assess the segmentation performance, the segmentation results are uploaded to the online evaluation system where the evaluation metrics dice score, positive predictive value(PPV), sensitivity, and kappa are used. The results demonstrate that the proposed method has good performance on the complete tumor region(dice: 0.83; PPV: 0.84; sensitivity: 0.82), while slightly worse performance on the tumor core(dice: 0.69; PPV: 0.76; sensitivity: 0.80) and enhancing tumor(dice: 0.58; PPV: 0.60; sensitivity: 0.65). It is competitive to the other groups in the brain tumor segmentation challenge. Therefore, it is a potential method in differentiation of healthy and pathological tissues.

Automated brain tumor segmentation from multimodal MRI data based on Tamura texture feature and an ensemble SVM classifier

Purpose–Theprecisesegmentation ofbraintumors isthe mostimportantandcrucialstepintheir diagnosis and treatment.Due to the presence of noise,uneven gray levels,blurred boundaries and edema around the brain tumor region,the brain tumor image has indistinct features in the tumor region,which pose a problem for diagnostics.The paper aims to discuss these issues.Design/methodology/approach–In this paper,the authors propose an original solution for segmentation using Tamura Texture and ensemble Support Vector Machine(SVM)structure.In the proposed technique,124 features of each voxel are extracted,including Tamura texture features and grayscale features.Then,these features are ranked using the SVM-Recursive Feature Elimination method,which is also adopted to optimize the parameters of the Radial Basis Function kernel of SVMs.Finally,the bagging random sampling method is utilized to construct the ensemble SVM classifierbased on a weighted voting mechanism to classify the types of voxel.Findings–The experiments are conducted over a sample data set to be called BraTS2015.The experiments demonstrate that Tamura texture is very useful in the segmentation of brain tumors,especially the feature of line-likeness.The superior performance of the proposed ensemble SVM classifier is demonstrated by comparison with single SVM classifiers as well as other methods.Originality/value–The authors propose an original solution for segmentation using Tamura Texture and ensemble SVM structure.

A Survey of MRI-Based Brain Tumor Segmentation Methods

Brain tumor segmentation aims to separate the different tumor tissues such as active cells, necrotic core,and edema from normal brain tissues of White Matter（WM）, Gray Matter（GM）, and Cerebrospinal Fluid（CSF）. MRIbased brain tumor segmentation studies are attracting more and more attention in recent years due to non-invasive imaging and good soft tissue contrast of Magnetic Resonance Imaging（MRI） images. With the development of almost two decades, the innovative approaches applying computer-aided techniques for segmenting brain tumor are becoming more and more mature and coming closer to routine clinical applications. The purpose of this paper is to provide a comprehensive overview for MRI-based brain tumor segmentation methods. Firstly, a brief introduction to brain tumors and imaging modalities of brain tumors is given. Then, the preprocessing operations and the state of the art methods of MRI-based brain tumor segmentation are introduced. Moreover, the evaluation and validation of the results of MRI-based brain tumor segmentation are discussed. Finally, an objective assessment is presented and future developments and trends are addressed for MRI-based brain tumor segmentation methods.

Double attention U-Net for brain tumor MR image segmentation

Purpose-Automatic segmentation of brain tumor from medical images is a challenging task because of tumor’s uneven and irregular shapes.In this paper,the authors propose an attention-based nested segmentation network,named DAU-Net.In total,two types of attention mechanisms are introduced to make the U-Net network focus on the key feature regions.The proposed network has a deep supervised encoder-decoder architecture and a redesigned dense skip connection.DAU-Net introduces an attention mechanism between convolutional blocks so that the features extracted at different levels can be merged with a task-related selection.Design/methodology/approach-In the coding layer,the authors designed a channel attention module.It marks the importance of each feature graph in the segmentation task.In the decoding layer,the authors designed a spatial attention module.It marks the importance of different regional features.And by fusing features at different scales in the same coding layer,the network can fully extract the detailed information of the original image and learn more tumor boundary information.Findings-To verify the effectiveness of the DAU-Net,experiments were carried out on the BRATS2018 brain tumor magnetic resonance imaging(MRI)database.The segmentation results show that the proposed method has a high accuracy,with a Dice similarity coefficient(DSC)of 89%in the complete tumor,which is an improvement of 8.04 and 4.02%,compared with fully convolutional network(FCN)and U-Net,respectively.Originality/value-The experimental results show that the proposed method has good performance in the segmentation of brain tumors.The proposed method has potential clinical applicability.

Deep learning network with Euclidean similarity factor for Brain MR Tumor segmentation and volume estimation

The major goal of this paper is to isolate tumor region from nontumor regions and the estimation of tumor volume.Accurate segmentation is not an easy task due to the varying size,shape and location of the tumor.After segmentation,volume estimation is necessary in order to accurately estimate the tumor volume.By exactly estimating the volume of abnormal tissue,physicians can do excellent prognosis,clinical planning and dosage estimation.This paper describes a new Euclidean Similarity factor(ESF)based active contour model with deep learning for segmenting the tumor region into complete,core and enhanced tumor portions.Initially,the ESF considers the spatial distances and intensity differences of the region automatically to detect the tumor region.It preserves the image details but removes the noisy details.Then,the 3D Convolutional Neural Network(3D CNN)segments the tumor by automatically extracting spatiotemporal features.Finally,the extended shoelace method estimates the volume of the tumor accurately for n-sided polygons.The simulation result achieves a high accuracy of 92%and Jaccard index of 0.912 and computes the tumor volume with effective performance than existing approaches.

Deep learning-based approach for segmentation of glioma subregions in MRI

Purpose-Brain tumor is one of the most dangerous and life-threatening disease.In order to decide the type of tumor,devising a treatment plan and estimating the overall survival time of the patient,accurate segmentation of tumor region from images is extremely important.The process of manual segmentation is very timeconsuming and prone to errors;therefore,this paper aims to provide a deep learning based method,that automatically segment the tumor region from MR images.Design/methodology/approach-In this paper,the authors propose a deep neural network for automatic brain tumor(Glioma)segmentation.Intensity normalization and data augmentation have been incorporated as pre-processing steps for the images.The proposed model is trained on multichannel magnetic resonance imaging(MRI)images.The model outputs high-resolution segmentations of brain tumor regions in the input images.Findings-The proposed model is evaluated on benchmark BRATS 2013 dataset.To evaluate the performance,the authors have used Dice score,sensitivity and positive predictive value(PPV).The superior performance of the proposed model is validated by training very popular UNet model in the similar conditions.The results indicate that proposed model has obtained promising results and is effective for segmentation of Glioma regions in MRI at a clinical level.Practical implications-The model can be used by doctors to identify the exact location of the tumorous region.Originality/value-The proposed model is an improvement to the UNet model.The model has fewer layers and a smaller number of parameters in comparison to the UNet model.This helps the network to train over databases with fewer images and gives superior results.Moreover,the information of bottleneck feature learned by the network has been fused with skip connection path to enrich the feature map.